// NewLabels returns labelblk Labels, a representation of externally usable subvolume
// or slice data, given some geometry and optional image data.
// If img is passed in, the function will initialize Voxels with data from the image.
// Otherwise, it will allocate a zero buffer of appropriate size.
//
// TODO : Unlike the standard imageblk.NewVoxels, the labelblk version can modify the
// labels based on the z-coordinate of the given geometry for Raveler labeling.
// This will be removed when Raveler-specific labels are moved outside DVID.
func (d *Data) NewLabels(geom dvid.Geometry, img interface{}) (*Labels, error) {
bytesPerVoxel := d.Properties.Values.BytesPerElement()
stride := geom.Size().Value(0) * bytesPerVoxel
var data []byte
if img == nil {
numVoxels := geom.NumVoxels()
if numVoxels <= 0 {
return nil, fmt.Errorf("Illegal geometry requested: %s", geom)
}
requestSize := int64(bytesPerVoxel) * numVoxels
if requestSize > server.MaxDataRequest {
return nil, fmt.Errorf("Requested payload (%d bytes) exceeds this DVID server's set limit (%d)",
requestSize, server.MaxDataRequest)
}
data = make([]byte, requestSize)
} else {
switch t := img.(type) {
case image.Image:
var inputBytesPerVoxel, actualStride int32
var err error
data, inputBytesPerVoxel, actualStride, err = dvid.ImageData(t)
if err != nil {
return nil, err
}
if actualStride != stride {
// Need to do some conversion here.
switch d.Labeling {
case Standard64bit:
data, err = d.convertTo64bit(geom, data, int(inputBytesPerVoxel), int(actualStride))
if err != nil {
return nil, err
}
case RavelerLabel:
data, err = d.addLabelZ(geom, data, actualStride)
if err != nil {
return nil, err
}
default:
return nil, fmt.Errorf("unexpected label type in labelblk: %s", d.Labeling)
}
}
case []byte:
data = t
actualLen := int64(len(data))
expectedLen := int64(bytesPerVoxel) * geom.NumVoxels()
if actualLen != expectedLen {
return nil, fmt.Errorf("labels data was %d bytes, expected %d bytes for %s",
actualLen, expectedLen, geom)
}
default:
return nil, fmt.Errorf("unexpected image type given to NewVoxels(): %T", t)
}
}
labels := &Labels{
imageblk.NewVoxels(geom, d.Properties.Values, data, stride),
}
return labels, nil
}
// Create a RGB interleaved volume.
func (d *Data) storeComposite(v dvid.VersionID, channels []*Channel) error {
// Setup the composite Channel
geom := channels[0].Geometry
pixels := int(geom.NumVoxels())
stride := geom.Size().Value(0) * 4
composite := &Channel{
Voxels: imageblk.NewVoxels(geom, compositeValues, channels[0].Data(), stride),
channelNum: channels[0].channelNum,
}
// Get the min/max of each channel.
numChannels := len(channels)
if numChannels > 3 {
numChannels = 3
}
var min, max [3]uint16
min[0] = uint16(0xFFFF)
min[1] = uint16(0xFFFF)
min[2] = uint16(0xFFFF)
for c := 0; c < numChannels; c++ {
channel := channels[c]
data := channel.Data()
beg := 0
for i := 0; i < pixels; i++ {
value := binary.LittleEndian.Uint16(data[beg : beg+2])
if value < min[c] {
min[c] = value
}
if value > max[c] {
max[c] = value
}
beg += 2
}
}
// Do second pass, normalizing each channel and storing it into the appropriate byte.
compdata := composite.Voxels.Data()
for c := 0; c < numChannels; c++ {
channel := channels[c]
window := int(max[c] - min[c])
if window == 0 {
window = 1
}
data := channel.Data()
beg := 0
begC := c // Channel 0 -> R, Channel 1 -> G, Channel 2 -> B
for i := 0; i < pixels; i++ {
value := binary.LittleEndian.Uint16(data[beg : beg+2])
normalized := 255 * int(value-min[c]) / window
if normalized > 255 {
normalized = 255
}
compdata[begC] = uint8(normalized)
beg += 2
begC += 4
}
}
// Set the alpha channel to 255.
alphaI := 3
for i := 0; i < pixels; i++ {
compdata[alphaI] = 255
alphaI += 4
}
// Store the result
return d.PutVoxels(v, composite.Voxels, nil)
}
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
timedLog := dvid.NewTimeLog()
// Get the action (GET, POST)
action := strings.ToLower(r.Method)
switch action {
case "get":
case "post":
default:
server.BadRequest(w, r, "Can only handle GET or POST HTTP verbs")
return
}
// Break URL request into arguments
url := r.URL.Path[len(server.WebAPIPath):]
parts := strings.Split(url, "/")
if len(parts[len(parts)-1]) == 0 {
parts = parts[:len(parts)-1]
}
if len(parts) < 4 {
server.BadRequest(w, r, "Incomplete API request")
return
}
// Process help and info.
switch parts[3] {
case "help":
w.Header().Set("Content-Type", "text/plain")
fmt.Fprintln(w, d.Help())
return
case "info":
jsonBytes, err := d.MarshalJSON()
if err != nil {
server.BadRequest(w, r, err)
return
}
w.Header().Set("Content-Type", "application/json")
fmt.Fprintf(w, string(jsonBytes))
return
default:
}
// Get the data name and parse out the channel number or see if composite is required.
var channelNum int32
channumStr := strings.TrimPrefix(parts[2], string(d.DataName()))
if len(channumStr) == 0 {
channelNum = 0
} else {
n, err := strconv.ParseInt(channumStr, 10, 32)
if err != nil {
server.BadRequest(w, r, "Error parsing channel number from data name '%s': %v", parts[2], err)
return
}
if int(n) > d.NumChannels {
minChannelName := fmt.Sprintf("%s1", d.DataName())
maxChannelName := fmt.Sprintf("%s%d", d.DataName(), d.NumChannels)
server.BadRequest(w, r, "Data only has %d channels. Use names '%s' -> '%s'", d.NumChannels,
minChannelName, maxChannelName)
return
}
channelNum = int32(n)
}
// Get the data shape.
shapeStr := dvid.DataShapeString(parts[3])
dataShape, err := shapeStr.DataShape()
if err != nil {
server.BadRequest(w, r, "Bad data shape given '%s'", shapeStr)
return
}
switch dataShape.ShapeDimensions() {
case 2:
sizeStr, offsetStr := parts[4], parts[5]
slice, err := dvid.NewSliceFromStrings(shapeStr, offsetStr, sizeStr, "_")
if err != nil {
server.BadRequest(w, r, err)
return
}
if action == "post" {
server.BadRequest(w, r, "DVID does not yet support POST of slices into multichannel data")
return
} else {
if d.NumChannels == 0 || d.Data.Values == nil {
server.BadRequest(w, r, "Cannot retrieve absent data '%d'. Please load data.", d.DataName())
return
}
values := d.Data.Values
if len(values) <= int(channelNum) {
server.BadRequest(w, r, "Must choose channel from 0 to %d", len(values))
return
}
stride := slice.Size().Value(0) * values.BytesPerElement()
dataValues := dvid.DataValues{values[channelNum]}
data := make([]uint8, int(slice.NumVoxels()))
v := imageblk.NewVoxels(slice, dataValues, data, stride)
channel := &Channel{
Voxels: v,
channelNum: channelNum,
}
img, err := d.GetImage(ctx.VersionID(), channel.Voxels, nil)
var formatStr string
if len(parts) >= 7 {
formatStr = parts[6]
}
//dvid.ElapsedTime(dvid.Normal, startTime, "%s %s upto image formatting", op, slice)
err = dvid.WriteImageHttp(w, img.Get(), formatStr)
if err != nil {
server.BadRequest(w, r, err)
return
}
}
case 3:
sizeStr, offsetStr := parts[4], parts[5]
_, err := dvid.NewSubvolumeFromStrings(offsetStr, sizeStr, "_")
if err != nil {
server.BadRequest(w, r, err)
return
}
if action == "get" {
server.BadRequest(w, r, "DVID does not yet support GET of volume data")
return
} else {
server.BadRequest(w, r, "DVID does not yet support POST of volume data")
return
}
default:
server.BadRequest(w, r, "DVID does not yet support nD volumes")
return
}
timedLog.Infof("HTTP %s: %s", r.Method, dataShape)
}
func (V3DRawMarshaler) UnmarshalV3DRaw(reader io.Reader) ([]*Channel, error) {
magicString := make([]byte, 24)
if n, err := reader.Read(magicString); n != 24 || err != nil {
return nil, fmt.Errorf("error reading magic string in V3D Raw file: %v", err)
}
if string(magicString) != "raw_image_stack_by_hpeng" {
return nil, fmt.Errorf("bad magic string in V3D Raw File: %s", string(magicString))
}
endianType := make([]byte, 1, 1)
if n, err := reader.Read(endianType); n != 1 || err != nil {
return nil, fmt.Errorf("could not read endianness of V3D Raw file: %v", err)
}
var byteOrder binary.ByteOrder
switch string(endianType) {
case "L":
byteOrder = binary.LittleEndian
case "B":
return nil, fmt.Errorf("cannot handle big endian byte order in V3D Raw File")
default:
return nil, fmt.Errorf("illegal byte order '%s' in V3D Raw File", endianType)
}
var dataType uint16
if err := binary.Read(reader, byteOrder, &dataType); err != nil {
return nil, err
}
var bytesPerVoxel int32
switch dataType {
case 1:
bytesPerVoxel = 1
case 2:
bytesPerVoxel = 2
default:
return nil, fmt.Errorf("cannot handle V3D Raw File with data type %d", dataType)
}
var width, height, depth, numChannels uint32
if err := binary.Read(reader, byteOrder, &width); err != nil {
return nil, fmt.Errorf("error reading width in V3D Raw File: %v", err)
}
if err := binary.Read(reader, byteOrder, &height); err != nil {
return nil, fmt.Errorf("error reading height in V3D Raw File: %v", err)
}
if err := binary.Read(reader, byteOrder, &depth); err != nil {
return nil, fmt.Errorf("error reading depth in V3D Raw File: %v", err)
}
if err := binary.Read(reader, byteOrder, &numChannels); err != nil {
return nil, fmt.Errorf("error reading # channels in V3D Raw File: %v", err)
}
// Allocate the V3DRaw struct for the # channels
totalBytes := int(bytesPerVoxel) * int(width*height*depth)
size := dvid.Point3d{int32(width), int32(height), int32(depth)}
volume := dvid.NewSubvolume(dvid.Point3d{0, 0, 0}, size)
v3draw := make([]*Channel, numChannels, numChannels)
var c int32
for c = 0; c < int32(numChannels); c++ {
data := make([]uint8, totalBytes, totalBytes)
var t dvid.DataType
switch bytesPerVoxel {
case 1:
t = dvid.T_uint8
case 2:
t = dvid.T_uint16
}
values := dvid.DataValues{
{
T: t,
Label: fmt.Sprintf("channel%d", c),
},
}
v := imageblk.NewVoxels(volume, values, data, int32(width)*bytesPerVoxel)
v3draw[c] = &Channel{
Voxels: v,
channelNum: c + 1,
}
}
// Read in the data for each channel
for c = 0; c < int32(numChannels); c++ {
if err := binary.Read(reader, byteOrder, v3draw[c].Data()); err != nil {
return nil, fmt.Errorf("error reading data for channel %d: %v", c, err)
}
}
return v3draw, nil
}